Contacts of the strand formed by residues 549 - 553 (chain A) in PDB entry 4WHH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 549 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A MET* 5.6 0.2 - - - +
405A CYS* 3.9 34.1 - - + +
542A ILE 4.0 0.8 - - - +
543A LEU* 3.6 3.5 - - - +
544A CYS* 3.0 32.2 + - + +
547A MET* 4.0 12.3 - - + +
548A ALA* 1.3 78.6 - - - +
550A VAL* 1.3 62.6 + - - +
561A THR* 4.4 2.9 - - + -
562A TYR 3.3 14.4 - - - +
563A ARG* 4.6 0.9 - - - -
564A LEU* 4.1 7.4 - - - +
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Residues in contact with VAL 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A LEU* 3.8 21.8 - - + -
542A ILE 3.4 6.1 - - - +
543A LEU* 3.7 26.2 - - + -
549A ALA* 1.3 75.5 - - - +
551A THR* 1.3 76.5 + - - +
552A TYR 4.7 0.2 - - - +
560A ARG 3.9 1.0 - - - +
561A THR* 3.3 2.8 - - - -
562A TYR* 2.8 51.1 + - + +
564A LEU* 3.9 18.6 - - + -
567A LEU* 4.1 14.8 - - + -
576A LEU* 5.0 4.3 - - + -
580A LEU* 4.2 8.5 - - + -
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Residues in contact with THR 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A CYS 4.8 0.3 + - - -
406A ILE* 5.9 1.1 - - + -
407A PRO* 3.4 24.0 - - + +
497A ILE* 4.7 7.0 - - + -
540A LYS 3.7 0.7 - - - +
541A LEU* 3.3 6.4 - - - -
542A ILE* 2.8 55.6 + - + +
550A VAL* 1.3 75.2 - - - +
552A TYR* 1.3 68.6 - - - +
553A ILE* 4.2 3.5 + - + -
559A PHE* 4.4 14.4 - - + -
560A ARG 3.4 11.9 - - - +
561A THR* 2.8 26.5 + - - +
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Residues in contact with TYR 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A GLN* 5.8 2.2 - - - -
539A THR* 3.5 22.2 - - - +
540A LYS 3.4 12.6 - - - -
541A LEU* 3.7 13.2 - - + -
550A VAL* 4.1 0.4 - - + -
551A THR* 1.3 72.8 - - - +
553A ILE* 1.3 72.9 + - - +
554A ASP* 3.8 22.7 - - + -
555A GLU* 3.8 8.3 + - - -
558A ASP 3.7 0.7 - - - +
559A PHE* 3.1 5.5 - - - -
560A ARG* 2.9 35.5 + - + +
562A TYR* 4.7 11.4 - + + -
575A GLU* 4.2 17.2 - - + +
576A LEU* 4.0 26.5 - - + -
579A ARG* 3.5 38.0 + - - -
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Residues in contact with ILE 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A TRP* 5.5 2.9 - - + +
493A ALA* 5.4 1.3 - - + -
494A GLY* 4.7 17.0 - - - +
497A ILE* 4.2 17.9 - - + -
538A HIS 5.0 3.1 - - - +
539A THR* 3.4 8.3 - - - -
540A LYS* 2.9 62.6 + - + +
542A ILE* 4.3 19.5 - - + -
551A THR* 4.6 5.2 - - + -
552A TYR* 1.3 77.8 - - - +
554A ASP* 1.3 68.8 + - - +
557A ARG* 4.0 22.7 - - + +
558A ASP 3.3 4.7 - - - +
559A PHE* 4.3 12.3 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il